Here's where to find the elusive drain plugs on your TJ.
First, you need to remove all the carpet from the tub. Then you can find them easier. They are black rubber plugs, and may prove somewhat difficult to remove the first time. There are a total of six. The easiest way to remove them is to use needle-nose pliers and grab the buggers. Carefully though, if you don't grab enough rubber, you might tear them.
Be sure to replace them securely, otherwise you may get water from the road leaking through.

Locate the ones in each footwell.
Driver:

Passenger:

Then there are two in the rear cargo area:

And one on each rear fender. Only the passenger side is shown, but they are identical:

i would be interested in knowing the best place to drill new drain plugs directly behind the front seats because that is where all my water tends to pool.

I just take a drill and put a 5/8" hole in the middle of where the water is pooling. Of course you have to look underneath first to make sure you don't drill through anything but the tub. My water pools differently depending on whether I park in the street or in the driveway because of how the jeep is tilted so there's no real science to it.

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behind the driver/passenger seats there is three channels on either side that lead directly to a plug. its not a rubber plug and if you remove it, it will be permanent. but i leave my carpets out and dont sit back there, and HATE the water pooling up so i took mine out. if you take a chizel start from the front of the vehicle direction and hammer into the oval plug. there is two tabs on each end underneath the jeep that will bend out when you hammer them out. the factory puts a protective coating, almost like putty, on the plug to keep water out, but it keeps it in. if you look at 98TJguy's pictures illustrating the front rubber plugs, you can see the plugs that are located at the bottoms of the channels. they are the same in the back. they come out very easy and i have had water to my hood and they drain MINT

behind the driver/passenger seats there is three channels on either side that lead directly to a plug. its not a rubber plug and if you remove it, it will be permanent. but i leave my carpets out and dont sit back there, and HATE the water pooling up so i took mine out. if you take a chizel start from the front of the vehicle direction and hammer into the oval plug. there is two tabs on each end underneath the jeep that will bend out when you hammer them out. the factory puts a protective coating, almost like putty, on the plug to keep water out, but it keeps it in. if you look at 98TJguy's pictures illustrating the front rubber plugs, you can see the plugs that are located at the bottoms of the channels. they are the same in the back. they come out very easy and i have had water to my hood and they drain MINT

THOSE are the plugs that DC should have made easily removable! The floor pan is designed to have the water drain out right there instead of where the smaller, round, rubber plugs are. I'd pull all those out if it wasn't permanent or if I could find an oval rubber plug to replace them with. If anyone has any ideas, I'd love to hear them.

THOSE are the plugs that DC should have made easily removable! The floor pan is designed to have the water drain out right there instead of where the smaller, round, rubber plugs are. I'd pull all those out if it wasn't permanent or if I could find an oval rubber plug to replace them with. If anyone has any ideas, I'd love to hear them.

EXACTLY. i didnt take all of mine out, just the two behind my seats, but in the winter i put my carpets back in so maybe ill take them all out

yeah i think its 97-02/03? that have two rubber in front, two on the "bed" area and two on the wheel wells. but i believe newer models have plugs behind the seats and we are stuck with a permanent removal